I have 2 D3s, the first has an August firmware and runs flawlessly, the 2nd came stock with 11/2 firmware and had the issue of one chain showing super high or super low temps.  It would alternate on reboot.  For me, installing the bitmain 11/20 firmware fixed the issue, all 3 chains are within a few degrees of each other now.  Side note, the 2nd D3 that came with newer firmware by default seems louder, and the fan speed % doesn't result in the same rpm as the 1st.  rpms on the 2nd are always higher when set to the same % as the 1st D3.

Next step after I run them both for a while on stock firmware to make sure there aren't other issues is to install Blissz firmware to save some on power and noise.